A primarily point of emigration was the village of Čekiškė, located about 24 kilometers from Kaunus on the Dubisda River and the main Kovno-Rasin road. It is an old settlement, founded at least by 1600. The village derived its name from an estate established in the mid-16th century. In 1738, Čekiškė was already mentioned as a town and was granted the privilege to hold markes and fairs in 1762.

The first mention of Jews associated with the town is from 1687; a Jew who rented an inn in Čekiškė was listed in the Vilkija inventory. By 1765, there was a synagogue. In 1783, two fires heavily destroyed the town, but a synagogue, a Jewish bathhouse, four breweries, and a Jewish house located between the square and the Lašiša rivulet, remained intact. Because buildings were made of wood, and heating and cooking relied on open flames, fires were common, with more fires reported in 1836, 1841 and 1887. The last was the fiercest and 66 houses, the post station, synagogue, and beit midrash were razed to the ground.

After the fire, only one synagogue was rebuilt – in fireproof brick! This building survives though remains vacant in is in deteriorated condition.

Before World War I there were about 200 Jewish families in the town but only about 60 families remained in the years before the Holocaust. These comprised about 45% of the total population.

Jews of Čekiškė worked in gardening and selling fruit and there were Jewish artisans and cartmen. Jews owned a steam-generated mill, sawmill and two tanneries. In the interwar period, there was a Jewish (Yiddish) primary school, a library, and a Jewish Peoples Bank with 60 members.

In the early days of the Nazi occupation, all Jews were ordered to leave their homes and move to a small ghetto established in the houses around the synagogue. Several days later, they were taken to the Jaučakiai forest near Vilkija and killed. According to the Nazi documents, 146 Čekiškė Jews were killed on September 4, 1941.